Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,428,079	C→T	pseudogene (386/402 nt) *213* (TAG→TAA)	ytfA → ytfB ←	pseudogene, related to transcriptional regulators OapA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,428,079	0	C	T	100.0%	120.5 / NA	38	pseudogene (386/402 nt) *213* (TAG→TAA)	ytfA ytfB	pseudogene, related to transcriptional regulators OapA family protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/19);  total (19/19)

ATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGTT  >  NC_000913/4427950‑4428207                                                                                                                                  |                                                                                                                                 attattTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCa                                                                                                                         >  1:241901/1‑139 (MQ=255)     tttGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCTCCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGaa                                                                                                                     <  2:159853/139‑1 (MQ=255)        gATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATaa                                                                                                                  >  1:760882/1‑139 (MQ=255)             aCCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCa                                                                                                                         <  2:800775/127‑1 (MQ=255)             aCCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCa                                                                                                                         >  1:800775/1‑127 (MQ=255)             aCCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTg                                                                                                             >  2:443061/1‑139 (MQ=255)                         ttGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTgg                                                                                                 >  1:759735/1‑139 (MQ=255)                            gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATTCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                              <  1:545515/139‑1 (MQ=255)                            gCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCgg                                                                                              >  1:597728/1‑139 (MQ=255)                                    tATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                                      <  2:241901/139‑1 (MQ=255)                                       cacaTCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGAc                                                                                   <  2:253234/139‑1 (MQ=255)                                          aTCAGTATGGTTTCACCCCAGGCGCTGTAAGCCAGACGTAAGGTCATCAAAGAGGCGATCCTTAGCTGGCTTTTGGTTGACGCTTCATTTACCGCGCACGAATAAAACTGCCAGCCGGATGGCGGGTGAACAGGTCCTg                                                                                <  1:143099/139‑1 (MQ=255)                                              gTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGa                                                                            <  2:745133/139‑1 (MQ=255)                                                aTGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGatt                                                                          >  1:340144/1‑139 (MQ=255)                                                aTGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGatt                                                                          <  2:546999/139‑1 (MQ=255)                                                 tGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGatta                                                                         <  1:570538/139‑1 (MQ=255)                                                 tGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGatta                                                                         <  1:687106/139‑1 (MQ=255)                                                      tCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTccc                                                                    >  1:205239/1‑139 (MQ=255)                                                             aGGCACTGGCAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                             <  1:553111/139‑1 (MQ=255)                                                             aGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                             <  1:414340/139‑1 (MQ=255)                                                             aGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                             <  2:633286/139‑1 (MQ=255)                                                              ggCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTCGACCCTTCATTTACC‑CGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAAt                                                           >  1:665554/1‑139 (MQ=255)                                                               gCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAAt                                                           <  2:759735/139‑1 (MQ=255)                                                                    ggAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGCACAGGACCTGTTGATTATTCCCCGTATCAATGGTTa                                                      >  2:503145/1‑139 (MQ=255)                                                                      aaGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAg                                                    <  2:340144/139‑1 (MQ=255)                                                                               gTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                             <  1:132512/121‑1 (MQ=255)                                                                               gTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCa                                                             >  2:132512/1‑121 (MQ=255)                                                                                       atcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCt                                   >  2:635092/1‑139 (MQ=255)                                                                                        tcaAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCACTGGTTAAGCCCGTCACCACGCCGCTg                                  >  1:271680/1‑139 (MQ=255)                                                                                         caAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTgg                                 >  1:144767/1‑139 (MQ=255)                                                                                               gaCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCt                           >  2:239530/1‑139 (MQ=255)                                                                                                aCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                                      >  2:482862/1‑79 (MQ=255)                                                                                                aCAATCCTTAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAg                                                                                      <  1:482862/79‑1 (MQ=255)                                                                                                   atcattAGCTGGCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCg                       <  1:342607/135‑1 (MQ=255)                                                                                                              gCTTTTGGTTGACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCa            >  1:154606/1‑139 (MQ=255)                                                                                                                        gACCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGtt  >  2:38676/1‑139 (MQ=255)                                                                                                                         aCCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCt                                                                                 >  2:391225/1‑59 (MQ=255)                                                                                                                         aCCCTTCATTTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCt                                                                                 <  1:391225/59‑1 (MQ=255)                                                                                                                                  |                                                                                                                                 ATTATTTGATCAACCAGCATACGCTTGGCCTGGTTTATCACATCAGTATGGTTTCACCCCAGGCACTGGAAGCCAGACGTAAGGTCATCAAAGAGACAATCCTTAGCTGGCTTTTGGTTGACCCTTCATCTACCGCGCACGAATAAAACTGCCATCCGGCTGGCGGGTGAACAGGACCTGTTGATTATTCCCCGTATCAATGGTTAAGCCCGTCACCACGCCGCTGGCGTTCTGGCGGATTTTCACCATCTGCCCGTT  >  NC_000913/4427950‑4428207

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑